Table 1

Public codon optimization softwares.

Name

Features

Comment

Reference


RE

Macintosh

[49]

GMAP

RE

[50]

CalcGene

CUT

[51]

COD OP

CUT, RE, DO

Unix perl

[52]

DNA Works

CUT, RE, DO

Web browser

[53]

Codon Optimizer

CUT, RE

[54]

Prot2DNA

CUT, RE, mSeq, Rep

Precursor to Gene Designer

[4]

Gene2Oligo

DO

Web browser

[55]

UpGene

CUT, DO

[56]

GeMS

CUT, RE, mSeq, DO

Web browser

[57]

JCat

CUT, RE

Web browser

[58]

Synthetic Gene Designer

CUT, RE, DO

Web browser

[59]


Software with features similar to the codon optimization module of Gene Designer. CUT indicates that one or more codon usage tables are referenced during reverse translation of the protein sequence. RE indicates that restriction endonuclease sites can be identified and silently removed and/or inserted. Rep indicates that repeats and/or inverted repeats can be silently removed. mSeq indicates that mRNA secondary structures can be silently removed. DO identifies software that includes a module for the design of oligonucleotides for gene synthesis

Villalobos et al. BMC Bioinformatics 2006 7:285   doi:10.1186/1471-2105-7-285

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